From 3c3ce9cd1f093779324241b9b74f7fdae41505fc Mon Sep 17 00:00:00 2001 From: Garrett Wright Date: Thu, 11 Jun 2026 08:55:57 -0400 Subject: [PATCH 1/2] Add molecules missing for cryosym work --- src/aspire/downloader/data_fetcher.py | 98 +++++++++++++++++++++++++++ src/aspire/downloader/registry.py | 21 ++++++ 2 files changed, 119 insertions(+) diff --git a/src/aspire/downloader/data_fetcher.py b/src/aspire/downloader/data_fetcher.py index 992298a4e1..a22529a690 100644 --- a/src/aspire/downloader/data_fetcher.py +++ b/src/aspire/downloader/data_fetcher.py @@ -288,6 +288,104 @@ def emdb_6458(): return vol +def emdb_14803(): + """ + Downloads the EMDB-14803 volume map and returns the file path. + + This molecule exhibits D3 symmetry. + + :return: A 'Volume' instance. + """ + file_path = fetch_data("emdb_14803.map") + vol = Volume.load(file_path, symmetry_group="D3") + + return vol + + +def emdb_3952(): + """ + Downloads the EMDB-3952 volume map and returns the file path. + + This molecule exhibits I symmetry. + + :return: A 'Volume' instance. + """ + file_path = fetch_data("emdb_3952.map") + vol = Volume.load(file_path, symmetry_group="I") + + return vol + + +def emdb_22308(): + """ + Downloads the EMDB-22308 volume map and returns the file path. + + This molecule exhibits D4 symmetry. + + :return: A 'Volume' instance. + """ + file_path = fetch_data("emdb_22308.map") + vol = Volume.load(file_path, symmetry_group="D4") + + return vol + + +def emdb_28025(): + """ + Downloads the EMDB-28025 volume map and returns the file path. + + This molecule exhibits D5 symmetry. + + :return: A 'Volume' instance. + """ + file_path = fetch_data("emdb_28025.map") + vol = Volume.load(file_path, symmetry_group="D5") + + return vol + + +def emdb_22358(): + """ + Downloads the EMDB-22358 volume map and returns the file path. + + This molecule exhibits D6 symmetry. + + :return: A 'Volume' instance. + """ + file_path = fetch_data("emdb_22358.map") + vol = Volume.load(file_path, symmetry_group="D6") + + return vol + + +def emdb_9571(): + """ + Downloads the EMDB-9571 volume map and returns the file path. + + This molecule exhibits D8 symmetry. + + :return: A 'Volume' instance. + """ + file_path = fetch_data("emdb_9571.map") + vol = Volume.load(file_path, symmetry_group="D8") + + return vol + + +def emdb_10920(): + """ + Downloads the EMDB-10920 volume map and returns the file path. + + This molecule exhibits D10 symmetry. + + :return: A 'Volume' instance. + """ + file_path = fetch_data("emdb_10920.map") + vol = Volume.load(file_path, symmetry_group="D10") + + return vol + + def simulated_channelspin(): """ Downloads the Simulated ChannelSpin dataset and returns the file path. diff --git a/src/aspire/downloader/registry.py b/src/aspire/downloader/registry.py index d96536d068..7baac9038f 100644 --- a/src/aspire/downloader/registry.py +++ b/src/aspire/downloader/registry.py @@ -13,6 +13,13 @@ "emdb_14621.map": "98363ae950229243131025995b5ba0486857ccb1256b3df8d25c1c282155238c", "emdb_2484.map": "6a324e23352bea101c191d5e854026162a5a9b0b8fc73ac5a085cc22038e1999", "emdb_6458.map": "645208af6d36bbd3d172c549e58d387b81142fd320e064bc66105be0eae540d1", + "emdb_14803.map": "sha256:10e1d3bbc11b6660c97b2ef8b654306c0a4c9a0c621386653f2464402ad1d20b", + "emdb_3952.map": "sha256:8367cd35fba18806b07b0461505c4588bd61ac6cdced5ebf51fa6f10e71559fa", + "emdb_22308.map": "sha256:2feceb32ec0cd645881e8a46957727c076a1711074e874860e94b7c0330c8201", + "emdb_28025.map": "sha256:64cd10920048bbd459d791523d65c20712b8fc199bdcdca1ce5cf6e0843d4364", + "emdb_22358.map": "sha256:b9dee4a27d92b7fe93ab6aa08087f9b4db8abc68ca553041061ad9c8cea05f54", + "emdb_9571.map": "sha256:e399b5a53c23e06e2384b15150ad1f9e6120a4799ea1fdfcaf213948d959bb65", + "emdb_10920.map": "sha256:8e08a511903d2f088b5ed69446843dad8214fa34128e513b90a3fc75cf3fa795", "simulated_channelspin.npz": "c0752674acb85417f6a77a28ac55280c1926c73fda9e25ce0a9940728b1dfcc8", } @@ -30,6 +37,13 @@ "emdb_14621.map": "https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-14621/map/emd_14621.map.gz", "emdb_2484.map": "https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-2484/map/emd_2484.map.gz", "emdb_6458.map": "https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-6458/map/emd_6458.map.gz", + "emdb_14803.map": "https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-14803/map/emd_14803.map.gz", + "emdb_3952.map": "https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-3952/map/emd_3952.map.gz", + "emdb_22308.map": "https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22308/map/emd_22308.map.gz", + "emdb_28025.map": "https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-28025/map/emd_28025.map.gz", + "emdb_22358.map": "https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-22358/map/emd_22358.map.gz", + "emdb_9571.map": "https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-9571/map/emd_9571.map.gz", + "emdb_10920.map": "https://ftp.ebi.ac.uk/pub/databases/emdb/structures/EMD-10920/map/emd_10920.map.gz", "simulated_channelspin.npz": "https://zenodo.org/records/8186548/files/example_FakeKV_dataset.npz", } @@ -47,5 +61,12 @@ "emdb_14621.map": "emdb_14621", "emdb_2484.map": "emdb_2484", "emdb_6458.map": "emdb_6458", + "emdb_14803.map": "emdb_14803", + "emdb_3952.map": "emdb_3952", + "emdb_22308.map": "emdb_22308", + "emdb_28025.map": "emdb_28025", + "emdb_22358.map": "emdb_22358", + "emdb_9571.map": "emdb_9571", + "emdb_10920.map": "emdb_10920", "simulated_channelspin.npz": "simulated_channelspin", } From 84b834ba1cf5a32e263ed43df03051baa62ffeef Mon Sep 17 00:00:00 2001 From: Garrett Wright Date: Mon, 15 Jun 2026 09:43:14 -0400 Subject: [PATCH 2/2] fixed incorrect doc strings. --- src/aspire/downloader/data_fetcher.py | 52 +++++++++++++-------------- 1 file changed, 26 insertions(+), 26 deletions(-) diff --git a/src/aspire/downloader/data_fetcher.py b/src/aspire/downloader/data_fetcher.py index a22529a690..efaadfe5a0 100644 --- a/src/aspire/downloader/data_fetcher.py +++ b/src/aspire/downloader/data_fetcher.py @@ -64,18 +64,18 @@ def fetch_data(dataset_name): def download_all(): """ - Download all ASPIRE example data and return a dictionary of filepaths. + Download all ASPIRE example data and return a dictionary of files. - :return: A dictionary of method names and associated file paths. + :return: A dictionary of method names and associated files. """ - file_paths = {} + items = {} for data_set in registry: - path = fetch_data(data_set) + item = fetch_data(data_set) name = file_to_method_map[data_set] - file_paths[name] = path + items[name] = item - return file_paths + return items def remove_downloads(): @@ -111,7 +111,7 @@ def emdb_2660(): def emdb_8012(): """ - Downloads the EMDB-8012 volume map and returns the file path. + Downloads the EMDB-8012 volume map and returns a `Volume` instance. The overall structure of the yeast spliceosomal U4/U6.U5 tri-snRNP at 3.7 Angstrom. @@ -125,7 +125,7 @@ def emdb_8012(): def emdb_2984(): """ - Downloads the EMDB-2984 volume map and returns the file path. + Downloads the EMDB-2984 volume map and returns a `Volume` instance. 2.2 A resolution cryo-EM structure of beta-galactosidase in complex with a cell-permeant inhibitor. This molecule exhibits D2 symmetry. @@ -140,7 +140,7 @@ def emdb_2984(): def emdb_8511(): """ - Downloads the EMDB-8511 volume map and returns the file path. + Downloads the EMDB-8511 volume map and returns a `Volume` instance. Structure of the human HCN1 hyperpolarization-activated cyclic nucleotide-gated ion channel. This molecule exhibits C4 symmetry. @@ -155,7 +155,7 @@ def emdb_8511(): def emdb_3645(): """ - Downloads the EMDB-3645 volume map and returns the file path. + Downloads the EMDB-3645 volume map and returns a `Volume` instance. CryoEM density of TcdA1 in prepore state (SPHIRE tutorial). This molecule exhibits C5 symmetry. @@ -170,7 +170,7 @@ def emdb_3645(): def emdb_4905(): """ - Downloads the EMDB-4905 volume map and returns the file path. + Downloads the EMDB-4905 volume map and returns a `Volume` instance. 3D structure of horse spleen apoferritin determined using multifunctional graphene supports for electron cryomicroscopy. This molecule exhibits octahedral symmetry. @@ -185,7 +185,7 @@ def emdb_4905(): def emdb_10835(): """ - Downloads the EMDB-10835 volume map and returns the file path. + Downloads the EMDB-10835 volume map and returns a `Volume` instance. High resolution cryo-EM structure of urease from the pathogen Yersinia enterocolitica. This molecule exhibits tetrahedral symmetry. @@ -200,7 +200,7 @@ def emdb_10835(): def emdb_5778(): """ - Downloads the EMDB-5778 volume map and returns the file path. + Downloads the EMDB-5778 volume map and returns a `Volume` instance. Structure of the capsaicin receptor, TRPV1, determined by single particle electron cryo-microscopy. This molecule exhibits C4 symmetry. @@ -215,7 +215,7 @@ def emdb_5778(): def emdb_6287(): """ - Downloads the EMDB-6287 volume map and returns the file path. + Downloads the EMDB-6287 volume map and returns a `Volume` instance. 2.8 Angstrom resolution reconstruction of the T20S proteasome. This molecule exhibits D7 symmetry. @@ -230,7 +230,7 @@ def emdb_6287(): def emdb_2824(): """ - Downloads the EMDB-2824 volume map and returns the file path. + Downloads the EMDB-2824 volume map and returns a `Volume` instance. Beta-galactosidase reconstruction. This molecule exhibits C2 symmetry. @@ -245,7 +245,7 @@ def emdb_2824(): def emdb_14621(): """ - Downloads the EMDB-14621 volume map and returns the file path. + Downloads the EMDB-14621 volume map and returns a `Volume` instance. Map of SARSCoV2 spike protein. This molecule exhibits C3 symmetry. @@ -260,7 +260,7 @@ def emdb_14621(): def emdb_2484(): """ - Downloads the EMDB-2484 volume map and returns the file path. + Downloads the EMDB-2484 volume map and returns a `Volume` instance. Pre-fusion structure of trimeric HIV-1 envelope glycoprotein determined by cryo-electron microscopy. This molecule exhibits C3 symmetry. @@ -275,7 +275,7 @@ def emdb_2484(): def emdb_6458(): """ - Downloads the EMDB-6458 volume map and returns the file path. + Downloads the EMDB-6458 volume map and returns a `Volume` instance. Cryo-EM Structure of the Activated NAIP2/NLRC4 Inflammasome Reveals Nucleated Polymerization. This molecule exhibits C11 symmetry. @@ -290,7 +290,7 @@ def emdb_6458(): def emdb_14803(): """ - Downloads the EMDB-14803 volume map and returns the file path. + Downloads the EMDB-14803 volume map and returns a `Volume` instance. This molecule exhibits D3 symmetry. @@ -304,7 +304,7 @@ def emdb_14803(): def emdb_3952(): """ - Downloads the EMDB-3952 volume map and returns the file path. + Downloads the EMDB-3952 volume map and returns a `Volume` instance. This molecule exhibits I symmetry. @@ -318,7 +318,7 @@ def emdb_3952(): def emdb_22308(): """ - Downloads the EMDB-22308 volume map and returns the file path. + Downloads the EMDB-22308 volume map and returns a `Volume` instance. This molecule exhibits D4 symmetry. @@ -332,7 +332,7 @@ def emdb_22308(): def emdb_28025(): """ - Downloads the EMDB-28025 volume map and returns the file path. + Downloads the EMDB-28025 volume map and returns a `Volume` instance. This molecule exhibits D5 symmetry. @@ -346,7 +346,7 @@ def emdb_28025(): def emdb_22358(): """ - Downloads the EMDB-22358 volume map and returns the file path. + Downloads the EMDB-22358 volume map and returns a `Volume` instance. This molecule exhibits D6 symmetry. @@ -360,7 +360,7 @@ def emdb_22358(): def emdb_9571(): """ - Downloads the EMDB-9571 volume map and returns the file path. + Downloads the EMDB-9571 volume map and returns a `Volume` instance. This molecule exhibits D8 symmetry. @@ -374,7 +374,7 @@ def emdb_9571(): def emdb_10920(): """ - Downloads the EMDB-10920 volume map and returns the file path. + Downloads the EMDB-10920 volume map and returns a `Volume` instance. This molecule exhibits D10 symmetry. @@ -388,7 +388,7 @@ def emdb_10920(): def simulated_channelspin(): """ - Downloads the Simulated ChannelSpin dataset and returns the file path. + Downloads the Simulated ChannelSpin dataset and returns a `Volume` instance. This dataset includes a stack of 54 volumes sized (54,54,54) and a corresponding stack of 10000 projection images (54,54).